Variant report

Variant	rs12541167
Chromosome Location	chr8:104245670-104245671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:104245583..104246168-chr8:104256525..104257469,2	MCF-7	breast:
2	chr8:104221105..104222852-chr8:104245322..104248174,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1138873	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12543038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12543973	0.84[TSI][hapmap]
rs13275377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13278361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13278540	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13279226	0.87[ASN][1000 genomes]
rs1353212	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1353213	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1403293	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1494278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1522707	0.89[MEX][hapmap];0.84[AMR][1000 genomes]
rs1568641	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16870243	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16870245	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16870249	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17205332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17799604	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1982892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1982893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2131860	0.83[MEX][hapmap]
rs2220825	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2270525	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs3104029	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3104031	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3104033	0.81[JPT][hapmap]
rs3107646	0.94[MEX][hapmap];0.89[AMR][1000 genomes]
rs3107648	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs3107649	0.80[AMR][1000 genomes]
rs3116457	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3116462	0.88[AMR][1000 genomes]
rs3116464	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3116466	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3116468	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs3133820	0.87[AMR][1000 genomes]
rs3133821	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3133824	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3133825	0.88[CEU][hapmap];0.80[AMR][1000 genomes]
rs3133833	0.81[JPT][hapmap]
rs3133835	1.00[ASW][hapmap]
rs3133836	1.00[ASW][hapmap]
rs3133837	0.81[JPT][hapmap]
rs34185273	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34201011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34273148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34337822	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4734693	0.90[ASN][1000 genomes]
rs4734695	0.90[ASN][1000 genomes]
rs7002269	0.95[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9656787	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831413	chr8:104085141-104269789	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	esv1848810	chr8:104128496-104369288	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv1844303	chr8:104128696-104369090	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1015965	chr8:104192086-104361108	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1017326	chr8:104236193-104313235	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12541167	SLC25A32	cis	cerebellum	SCAN
rs12541167	BAALC	cis	parietal	SCAN
rs12541167	FZD6	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104242400-104251200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:104242400-104251200	Weak transcription	HMEC	breast
3	chr8:104242800-104250200	Weak transcription	Fetal Brain Female	brain
4	chr8:104243200-104248600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr8:104243800-104246400	Weak transcription	Psoas Muscle	Psoas
6	chr8:104243800-104248000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr8:104243800-104248000	Weak transcription	Osteobl	bone
8	chr8:104243800-104248200	Weak transcription	NHLF	lung
9	chr8:104244000-104251200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr8:104244000-104268400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr8:104244200-104248000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr8:104244200-104251400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr8:104244600-104257400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr8:104245000-104248200	Weak transcription	NHDF-Ad	bronchial
15	chr8:104245200-104245800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr8:104245200-104247000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr8:104245600-104254800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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